From: upayan baul (margheritan22_at_gmail.com)
Date: Mon Sep 14 2015 - 06:59:00 CDT
Dear NAMD users,
Sorry for the long mail. I wished to let you know the things I have already
tried.
I wish to simulate a system with stacked graphene sheets (with bonds across
boundaries in XY) in water in an NPT ensemble. The initial configuration of
the
system is shown in.
https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_init.jpg
As an ideal test case, I wish to retain the planarity of the graphene
sheets to as great a
degree as possible.
I am using atom type CA and corresponding parameters for bond, angle,
dihedral
and nonbonded interactions from CHARMM protein parameters (par_all22_prot).
I
have tried small simulations
without impropers : (based on Kenno's suggestion that impropers only
over-rigidify 6
membered ring structures
http://www.charmm.org/ubbthreads/ubbthreads.php?ubb=showflat&Number=33962 )
which resulted in a configuration as shown (periodic) in:
https://www.imsc.res.in/~upayanb/graphene_namd/no_improper/graphene_wat_fin.jpg
with impropers: (based on Axel's suggestion (though this might be for the
finite-sheet case,
I might have misunderstood) to include impropers for planarity
http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/19410.html )
which resulted in a configuration as shown in:
https://www.imsc.res.in/~upayanb/graphene_namd/with_improper/graphene_wat_fin_impropers.jpg
in which I have used an additional improper interaction of
!atom types Kpsi psi0
CA CA CA CA 10.0 0 0.00
Neither of the two cases are resulting in highly planar structures.
Increasing Kpsi is resulting
in more puckered structures (for Kpsi > 20, the simulations are crashing
with statements like
ERROR: Atoms moving too fast; simulation has become unstable (3 atoms on
patch 1 pe 0).
How can I obtain a more planar configuration for graphene? I have tried
fixed atom simulations.
In NPT, without constant area such simulations crash owing to fixed atom at
boundaries. With
constant area, the system expands in the Z- direction, causing the water to
move away from the
surface.
Thanking you,
Upayan
S.R.F., Physics
IMSc
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